That's one of the main problems with grasping exactly what we mean by "c'est", because it is used in many different situations which all require different translations in English.

C'est is an impersonal way of describing almost anything, and can introduce a nominal group (like in your example, "une fille sympa" is a group with a noun) of any gender (you can absolutely say "c'est un garçon sympa", which would then translate to "he's a nice boy"). It would be the equivalent of saying in English: "That's a nice dog", just with an extended version that can also introduce a person in the same way. In both cases the adjective has to agree with the noun it follows or precedes.

However, when it introduces an adjective (like in the above example), then it's meant as "It's short" or "That's short", and can be expressed to describe anything, with "cela" or "ça" shortened to "c'" and replacing anything that was previously mentioned, and always impersonal, staying in the masculine singular form.

You also have to remember that our use of "court" never applies to the height of a person, for which we use the adjective "petit" (small). This sentence can therefore not be meant for a person, but rather relates to the length of something else.